Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
7,325 results • Page
5 of 147
Sort: replies
Rank
Views
Votes
Replies
17
votes
14
replies
9.6k
views
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
ATAC-seq
next-gen
R
updated 3 months ago by
QX
▴ 60 • written 6.1 years ago by
a.rex
▴ 350
3
votes
14
replies
2.0k
views
7 follow
Some lines are not well organized in BED file, how to correct them ? Thanks a lot !
BED
updated 11 months ago by
Alex Reynolds
36k • written 11 months ago by
Tom
• 0
16
votes
14
replies
15k
views
9 follow
Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed Genes) to confirm results together- is it a good idea?
RNA-Seq
R
sequencing
updated 9 weeks ago by
arnaud_p
• 0 • written 4.4 years ago by
chokevin8
▴ 30
12
votes
13
replies
12k
views
11 follow
how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
rna-seq
updated 8 weeks ago by
F
• 0 • written 7.1 years ago by
lhaiyan3
▴ 80
4
votes
13
replies
1.5k
views
Mapping FASTQ files of scRNA-seq to reference genome
star
EBI
cellranger
scRNA-seq
SRA
updated 11 months ago by
Ram
44k • written 11 months ago by
Researcher
▴ 20
4
votes
13
replies
1.9k
views
8 follow
Failed to download data from EBI BioStudies with ascp/Aspera
aspera
EBI
updated 4 months ago by
Aster
• 0 • written 8 months ago by
biock
▴ 70
2
votes
13
replies
5.1k
views
8 follow
scatter plot for DAPC
snp
updated 11 weeks ago by
Myosotis1979
▴ 30 • written 5.3 years ago by
evelyn
▴ 230
10
votes
13
replies
3.4k
views
Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
ChIP-seq
spike-in
scaling-factor
coverage
3 months ago by
kalavattam
▴ 280
9
votes
13
replies
1000
views
7 follow
Nextflow process not executing
STAR-mapping.
Nextflow
5 months ago by
myoui3122010
▴ 20
4
votes
13
replies
1.9k
views
7 follow
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
DEG
limma
rstudio
updated 6 months ago by
GenoMax
148k • written 6 months ago by
egascon
▴ 60
3
votes
13
replies
1.5k
views
Blastn produce a single ouput file instead of multiple output files
blastn
updated 11 months ago by
Ram
44k • written 11 months ago by
neha.jnu463
• 0
4
votes
13
replies
1.4k
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 7 months ago by
BioinfGuru
★ 2.1k • written 8 months ago by
matteo.levorato
• 0
6
votes
13
replies
11k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 8 months ago by
Mike Smith
★ 2.1k • written 3.4 years ago by
lincaijin1994
▴ 50
4
votes
13
replies
917
views
6 follow
featureCounts segmentation fault
featureCounts
pipeline
RNA-Seq
9 weeks ago by
Jaber
▴ 30
9
votes
13
replies
4.5k
views
error when running bbduk
bbduk
updated 5 months ago by
Ram
44k • written 3.4 years ago by
Lila M
★ 1.3k
6
votes
13
replies
5.0k
views
11 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 25 days ago by
janneke.aylward
▴ 20 • written 3.5 years ago by
pmc.sa
▴ 40
12
votes
13
replies
5.0k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 8 months ago by
Ram
44k • written 6.8 years ago by
firestar
★ 1.6k
0
votes
13
replies
4.3k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 7 months ago by
drstalinantony28
• 0 • written 2.8 years ago by
ymj
▴ 10
6
votes
13
replies
1.2k
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
8 months ago by
Maverick
▴ 10
9
votes
13
replies
1.1k
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 6 months ago by
gglim
▴ 210 • written 6 months ago by
Assa Yeroslaviz
★ 1.9k
11
votes
13
replies
13k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 6 months ago by
May Ling
▴ 10 • written 2.9 years ago by
wmsalsah
▴ 10
1
vote
13
replies
985
views
Error with plotMDS in R
plotMDS
RStudio
4 months ago by
egascon
▴ 60
0
votes
13
replies
1.4k
views
Help with the new nomenclature of multi-nucleotide variants
bam
igv
multinucleotide
9 months ago by
amy__
▴ 220
12
votes
13
replies
6.8k
views
7 follow
Centrimo error: Template does not contain data section
ChIP-Seq
MEME
updated 5 months ago by
Johan Zicola
▴ 70 • written 5.2 years ago by
Matus
▴ 70
75
votes
13
replies
68k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
classification
r
cancer
randomForest
machine-learning
updated 4 months ago by
Obi Griffith
20k • written 11.1 years ago by
Nicholas Spies
★ 1.2k
42
votes
13
replies
29k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 9 months ago by
CTLong
▴ 120 • written 7.1 years ago by
Sreeraj Thamban
▴ 300
5
votes
13
replies
2.6k
views
6 follow
GATK memory error with Java
GATK
VCF
SNP
Java
5 months ago by
anikcropscience
▴ 260
32
votes
13
replies
10k
views
11 follow
Any Recommendations For Statistical Genetics Texts?
genetics
statistics
gwas
updated 11 months ago by
Angelo
• 0 • written 14.3 years ago by
Shigeta
▴ 180
31
votes
13
replies
12k
views
9 follow
Variant Function Prediction
variant-effect
SNP
updated 3 months ago by
Ram
44k • written 10.7 years ago by
User 1933
▴ 360
13
votes
13
replies
19k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna
protein
updated 8 months ago by
ummeswaiba
• 0 • written 10.9 years ago by
biostar
▴ 170
36
votes
13
replies
7.6k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data
galaxy
written 13.6 years ago by
Pi
▴ 520
0
votes
13
replies
1.9k
views
Error in schicexplorer's hicbuildmatrix
hicbuildmatrix
schic
updated 11 months ago by
ATpoint
85k • written 12 months ago by
1125195245
• 0
9
votes
13
replies
2.4k
views
BBduk ftm parameter
BBduk
parameters
updated 10 months ago by
Swatilekha
• 0 • written 6.3 years ago by
lieven.sterck
15k
7
votes
13
replies
5.2k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 7 months ago by
ATpoint
85k • written 7 months ago by
BioinfGuru
★ 2.1k
47
votes
13
replies
18k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 9 months ago by
Konstantinos
• 0 • written 4.2 years ago by
Hamid Ghaedi
3.3k
12
votes
13
replies
18k
views
6 follow
Cluster sub-set analysis using Seurat
seurat
single-cell
updated 12 months ago by
j.gleixner
▴ 30 • written 4.4 years ago by
singcell
• 0
4
votes
13
replies
1.1k
views
Can't reproduce harmony results in Seurat
Seurat
scRNA-seq
harmony
12 weeks ago by
fifty_fifty
▴ 70
9
votes
13
replies
5.4k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 7 months ago by
analyst
▴ 50 • written 7.0 years ago by
David_emir
▴ 500
4
votes
13
replies
1.2k
views
BBMap Excess Fold Coverage
bbmap
updated 4 months ago by
GenoMax
148k • written 5 months ago by
shacon
• 0
7
votes
13
replies
2.9k
views
How to convert raw Nanopore R9 fast5 files to fastq files ?
dorado
fast5
basecalling
nanopore
updated 6 weeks ago by
lieven.sterck
15k • written 9 months ago by
Lélé
▴ 10
16
votes
13
replies
16k
views
9 follow
How to work out Z score for heatmaps for RNA seq dataset
R
updated 6 months ago by
robert.flynn.21
▴ 10 • written 3.6 years ago by
v.johnson
▴ 30
25
votes
13
replies
1.1k
views
6 follow
Forum:
How to do datamining in bioinformatics
data-mining
updated 8 weeks ago by
LauferVA
4.5k • written 8 weeks ago by
Biomed-jeh
▴ 70
9
votes
13
replies
1.9k
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 6 months ago by
i.sudbery
20k • written 7 months ago by
Estevão
▴ 10
15
votes
13
replies
6.6k
views
8 follow
Forum:
Does a PhD or work experience set you up better to do bioinformatics work in industry?
advice
industry
phd
updated 11 months ago by
benformatics
4.0k • written 2.1 years ago by
buhbs
▴ 30
9
votes
12
replies
1.5k
views
Is it possible to access the code of a bioinformatics article?
publication
updated 10 months ago by
Zhenyu Zhang
★ 1.2k • written 10 months ago by
sil_bioinfo
▴ 50
9
votes
12
replies
1.7k
views
BUSCO duplicated
BUSCO
Trinity
updated 11 months ago by
GenoMax
148k • written 11 months ago by
sansan96
▴ 130
11
votes
12
replies
1.4k
views
dedup STAR transcriptome file using umi_tools
rna-seq
umi
transcriptome
umi_tools
4 weeks ago by
ATRX
★ 1.1k
1
vote
12
replies
5.8k
views
7 follow
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 5 weeks ago by
jurriaanjanssen
• 0 • written 2.2 years ago by
Manav
• 0
0
votes
12
replies
1.5k
views
BWA Index Referencing Failed. Possible Reason and Solutions?
BWA
updated 10 months ago by
a.alnawfal.1992
▴ 360 • written 11 months ago by
Tundup
• 0
0
votes
12
replies
871
views
Creating a sample specific directory on the go while using -wget command to download the files
wget
ncbi
updated 5 months ago by
Ram
44k • written 5 months ago by
Hrituraj
• 0
7,325 results • Page
5 of 147
Recent Votes
Answer: pvalueCutoff for enrichGO, enrichKEGG and enrichDO does not seem to function pro
Answer: How to remove pseudo genes from a list
Comment: Database like Cellxgene for well-annotated atlas
Comment: Database like Cellxgene for well-annotated atlas
Answer: m6A modification prediction using Nanopore DRS data (RNA004)
Answer: m6A modification prediction using Nanopore DRS data (RNA004)
Answer: Dorado for m6A modification detection
Recent Locations •
All
Mexico,
just now
United States,
1 minute ago
Seattle, WA USA,
1 minute ago
United States,
4 minutes ago
Saudi Arabia,
8 minutes ago
Australia,
10 minutes ago
Australia,
10 minutes ago
Recent Awards •
All
Scholar
to
GenoMax
148k
Popular Question
to
George
▴ 10
Teacher
to
dsull
★ 7.0k
Teacher
to
Pierre Lindenbaum
164k
Student
to
RoyBatty
▴ 30
Popular Question
to
FJCF
• 0
Popular Question
to
DGTool
▴ 290
Recent Replies
Comment: question about seurat figure PC_heatmap
by
rohitsatyam102
▴ 920
What about the colors. How do you interpret them?
Comment: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
★ 7.7k
I am not the appropriate person to respond to a detailed question of this type. If you want to submit a (potential) bug report to the featu…
Comment: Seurat Mito Prefix Removed from Features
by
Koki
• 0
Thank you for the correction. I mistook Atp8a1 with MT-ATP8, but I am still interested in removing mitochondrial genes. I an analyzing GSM3…
Answer: Seurat Mito Prefix Removed from Features
by
LChart
4.6k
Atp8a1 is a nuclear-transcribed gene (chr4 in humans). Typically one is interested in removing mitochondrially-transcribed genes (chrM). Ar…
Comment: How to remove pseudo genes from a list
by
Meghan.T
• 0
Great! Thank you very much!
Comment: dorado and modkit for m6A identification
by
GenoMax
148k
Check `modkit dmr` for differential analysis as shown here: https://github.com/nanoporetech/modkit/blob/master/book/src/advanced_usage.md
Comment: Database like Cellxgene for well-annotated atlas
by
Laker Chandler
• 0
Thank you, ATpoint and Jared. Yes, I am now looking for dataset for mouse immune cells in blood or lymph nodes. Ideally, we want to find im…
Comment: m6A modification prediction using Nanopore DRS data (RNA004)
by
baibhu1234
• 0
hi @genomax i was able to run dorado finally time dorado basecaller rna004_130bps_hac\@v5.1.0 /pod5/ --modified-bases-models r…
Comment: Database like Cellxgene for well-annotated atlas
by
ATpoint
85k
> All just really depends Exactly. The same goes for gene signatures in general. You get vastly different marker genes if you compare for …
Comment: Database like Cellxgene for well-annotated atlas
by
ATpoint
85k
ImmGen is very detailed. They have a particular focus on lymphoid cells and (FACS-)enriched a lot of subsets from (e.g.) T cells in differe…
Comment: Can I trust this script I wrote for assembling plant genomes?
by
Michael
55k
I'd second that. It will also solve problems of re-entrance, reproducibility, and software versions with less code. On the other hand, it c…
Comment: Database like Cellxgene for well-annotated atlas
by
jared.andrews07
★ 18k
The Immgen site is a bit of a mess. Probably easy to cross-reference the labels [directly from GEO](https://www.ncbi.nlm.nih.gov/geo/query/…
Comment: Database like Cellxgene for well-annotated atlas
by
jared.andrews07
★ 18k
Depends entirely on your needs and tissue. The Monaco set in celldex is expansive, easy to interpret, and covers a lot of bases for human i…
Comment: Database like Cellxgene for well-annotated atlas
by
Laker Chandler
• 0
Jarad, thank you! You wound to have vast experience. Could you share with your person experience with these options when you have time. I w…
Comment: Database like Cellxgene for well-annotated atlas
by
zhai
• 0
Thank you very much!! Would you mind give me more hint on how to find the annotation information of the dataset on immgen?
Traffic: 1684 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6